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Coexpression cluster:C622: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.18943,0.1536,0.183956,0.806989,0.153879,0.296522,0.360887,0.270053,0.0771434,0.586318,0.271739,1.03072,0.20272,0.925865,0.907585,0.506197,0.560096,0.752071,0.0612687,0.403976,0.541421,0.121811,0.290113,0.150321,0.218509,1.07436,0.0456804,0.288329,0.472898,0.152963,0.706977,0.594213,0.320109,0.205943,0.130292,0.139795,0.12818,0.29748,0.363308,0.881025,0.806754,0.241157,0.495734,0.151865,0.664236,0.206995,0.361827,0.262957,0.456684,0.473123,0.431291,0.372023,0.780607,0.666176,0.811691,0.353512,0.15913,0.325599,0.152817,0.324748,0.632472,0.363871,0.564331,0.534578,0.379438,0.503101,0.896916,1.25738,0.584559,1.09778,0.652781,0.585859,0.103789,0.80977,0.196336,0.402042,0.368241,0.519091,0.581542,0.61268,0.227702,0.533593,0.37913,0.274429,0.760489,0.0478103,1.7691,0.146775,0.454557,1.35556,0.98765,0.734737,0.609873,0.331798,0.154399,0.71683,0.476274,0.649779,1.16091,0.552868,0.73791,0.6046,0.644537,0.563483,0.492631,0.268065,0.548871,0.348037,0.218314,0.142849,0.19228,0.641937,0.531469,1.3989,0.940917,0.12714,0.0638634,0.704759,0.500972,0.102878,0.801818,0.452379,0.294241,1.78671,1.04884,0.519787,0.355419,0.614537,0.842806,0.719563,0.735394,0.256408,0.856671,0.386057,1.00021,0.588214,0.249339,0.288795,0.95886,1.80749,1.40745,0.922589,0.356906,0.646464,0.494226,0.318465,0.47912,1.64894,1.2469,0.0991414,0.712398,0.0473433,0.735758,0.541074,0.363452,1.12781,0.440071,0.443316,0.218554,0.196611,0.921409,0.718143,0.580811,0.199028,0.508869,0.378443,0.0919059,0.35974,0.0337609
|tfbs_overrepresentation_jaspar=MA0003.1;0.080891,MA0004.1;0.757232,MA0006.1;0.906232,MA0007.1;0.260673,MA0009.1;0.695988,MA0014.1;0.045605,MA0017.1;0.181071,MA0019.1;1.04045,MA0024.1;0.59663,MA0025.1;0.824398,MA0027.1;2.28954,MA0028.1;0.164086,MA0029.1;0.614815,MA0030.1;0.604021,MA0031.1;0.543644,MA0038.1;0.363295,MA0040.1;0.620334,MA0041.1;0.291389,MA0042.1;0.264992,MA0043.1;0.69629,MA0046.1;0.685589,MA0048.1;0.267987,MA0050.1;0.73369,MA0051.1;0.944936,MA0052.1;0.623986,MA0055.1;0.148782,MA0056.1;0,MA0057.1;0.0243088,MA0058.1;0.580064,MA0059.1;0.57771,MA0060.1;0.0773489,MA0061.1;1.27348,MA0063.1;0,MA0066.1;0.363668,MA0067.1;1.00375,MA0068.1;0.0444239,MA0069.1;0.681911,MA0070.1;0.671241,MA0071.1;0.329767,MA0072.1;0.666958,MA0073.1;0.0596341,MA0074.1;0.358953,MA0076.1;0.609177,MA0077.1;0.65962,MA0078.1;0.447828,MA0081.1;0.578007,MA0083.1;0.703169,MA0084.1;1.18798,MA0087.1;0.664629,MA0088.1;0.0514785,MA0089.1;0,MA0090.1;0.635809,MA0091.1;1.39427,MA0092.1;0.691297,MA0093.1;0.915249,MA0095.1;0,MA0098.1;0,MA0100.1;0.375452,MA0101.1;2.12227,MA0103.1;0.146091,MA0105.1;0.701161,MA0106.1;1.0329,MA0107.1;1.16768,MA0108.2;0.540797,MA0109.1;0,MA0111.1;0.660878,MA0113.1;0.414278,MA0114.1;0.104181,MA0115.1;0.929032,MA0116.1;0.10959,MA0117.1;0.732,MA0119.1;0.548507,MA0122.1;0.756889,MA0124.1;0.888592,MA0125.1;0.807083,MA0130.1;0,MA0131.1;0.464307,MA0132.1;0,MA0133.1;0,MA0135.1;0.725055,MA0136.1;0.369468,MA0139.1;0.0564547,MA0140.1;0.327488,MA0141.1;0.197753,MA0142.1;0.514195,MA0143.1;0.414436,MA0144.1;0.316332,MA0145.1;0.16253,MA0146.1;0.248894,MA0147.1;0.36013,MA0148.1;0.296708,MA0149.1;0.319221,MA0062.2;0.0599644,MA0035.2;0.326883,MA0039.2;0.00412151,MA0138.2;0.44894,MA0002.2;0.0708857,MA0137.2;0.168782,MA0104.2;0.561843,MA0047.2;1.00935,MA0112.2;1.10559,MA0065.2;0.16797,MA0150.1;1.17219,MA0151.1;0,MA0152.1;0.333125,MA0153.1;0.790794,MA0154.1;0.0872435,MA0155.1;0.0505475,MA0156.1;0.170442,MA0157.1;0.489002,MA0158.1;0,MA0159.1;0.361202,MA0160.1;0.30953,MA0161.1;0,MA0162.1;0.0826011,MA0163.1;0.0183776,MA0164.1;0.425415,MA0080.2;0.154815,MA0018.2;0.400879,MA0099.2;0.333432,MA0079.2;4.50435e-05,MA0102.2;1.22472,MA0258.1;1.04518,MA0259.1;0.117259,MA0442.1;0
}}
}}

Revision as of 19:19, 22 January 2013


Full id: C622_CD19_CD14_immature_Peripheral_Neutrophils_Natural_CD8



Phase1 CAGE Peaks

Hg19::chr11:6633799..6633813,-p11@TAF10
Hg19::chr16:19222406..19222410,-p@chr16:19222406..19222410
-
Hg19::chr1:1005339..1005350,-p@chr1:1005339..1005350
-
Hg19::chr1:179050670..179050709,+p3@TOR3A
Hg19::chr1:226298353..226298372,-p@chr1:226298353..226298372
-
Hg19::chr2:33701603..33701615,-p@chr2:33701603..33701615
-
Hg19::chr2:88905814..88905819,-p@chr2:88905814..88905819
-
Hg19::chr2:88909458..88909464,-p1@AK129635
Hg19::chr4:103680719..103680723,-p@chr4:103680719..103680723
-
Hg19::chr5:149790235..149790248,-p@chr5:149790235..149790248
-
Hg19::chr6:14127098..14127123,+p@chr6:14127098..14127123
+
Hg19::chr6:14127175..14127200,+p@chr6:14127175..14127200
+
Hg19::chr6:167507740..167507764,+p@chr6:167507740..167507764
+
Hg19::chr8:102218459..102218472,-p8@ZNF706


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

GO IDGO nameFDR corrected p-value
GO:0051085chaperone cofactor-dependent protein folding0.0334245397562372
GO:0006458'de novo' protein folding0.0334245397562372
GO:0051084'de novo' posttranslational protein folding0.0334245397562372
GO:0005669transcription factor TFIID complex0.0469838878480247



Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br>disease_data<br>

Cell Type
Ontology termp-valuen
leukocyte2.07e-85136
nongranular leukocyte2.01e-67115
hematopoietic stem cell4.28e-67168
angioblastic mesenchymal cell4.28e-67168
hematopoietic cell2.30e-66177
hematopoietic lineage restricted progenitor cell3.97e-66120
hematopoietic oligopotent progenitor cell1.80e-58161
hematopoietic multipotent progenitor cell1.80e-58161
classical monocyte2.34e-4942
CD14-positive, CD16-negative classical monocyte2.34e-4942
defensive cell7.99e-4248
phagocyte7.99e-4248
myeloid leukocyte1.26e-4172
granulocyte monocyte progenitor cell5.80e-4167
macrophage dendritic cell progenitor8.42e-3961
myeloid lineage restricted progenitor cell6.00e-3766
monopoietic cell1.63e-3559
monocyte1.63e-3559
monoblast1.63e-3559
promonocyte1.63e-3559
myeloid cell4.93e-31108
common myeloid progenitor4.93e-31108
lymphocyte5.98e-2553
common lymphoid progenitor5.98e-2553
nucleate cell1.01e-2355
lymphoid lineage restricted progenitor cell1.04e-2352
mesenchymal cell1.28e-20354
connective tissue cell8.26e-20361
lymphocyte of B lineage1.17e-1924
pro-B cell1.17e-1924
stuff accumulating cell2.00e-1887
motile cell5.73e-17386
stem cell7.95e-14441
multi fate stem cell1.61e-13427
dendritic cell1.95e-1310
somatic stem cell4.79e-13433
B cell9.86e-1114
intermediate monocyte1.00e-109
CD14-positive, CD16-positive monocyte1.00e-109
Langerhans cell4.31e-105
conventional dendritic cell5.13e-108
circulating cell6.71e-096
natural killer cell6.23e-083
pro-NK cell6.23e-083
single nucleate cell1.52e-073
mononuclear cell1.52e-073
basophil2.65e-073
plasmacytoid dendritic cell3.55e-073
Uber Anatomy
Ontology termp-valuen
hematopoietic system7.81e-4198
blood island7.81e-4198
hemolymphoid system2.67e-37108
bone marrow1.09e-3676
immune system1.37e-3593
bone element4.19e-3382
skeletal element4.49e-2990
skeletal system5.92e-25100
connective tissue1.04e-18371
lateral plate mesoderm1.83e-12203
musculoskeletal system2.23e-10167
Disease
Ontology termp-valuen
lymphoma4.49e-0810


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.10.080891
MA0004.10.757232
MA0006.10.906232
MA0007.10.260673
MA0009.10.695988
MA0014.10.045605
MA0017.10.181071
MA0019.11.04045
MA0024.10.59663
MA0025.10.824398
MA0027.12.28954
MA0028.10.164086
MA0029.10.614815
MA0030.10.604021
MA0031.10.543644
MA0038.10.363295
MA0040.10.620334
MA0041.10.291389
MA0042.10.264992
MA0043.10.69629
MA0046.10.685589
MA0048.10.267987
MA0050.10.73369
MA0051.10.944936
MA0052.10.623986
MA0055.10.148782
MA0056.10
MA0057.10.0243088
MA0058.10.580064
MA0059.10.57771
MA0060.10.0773489
MA0061.11.27348
MA0063.10
MA0066.10.363668
MA0067.11.00375
MA0068.10.0444239
MA0069.10.681911
MA0070.10.671241
MA0071.10.329767
MA0072.10.666958
MA0073.10.0596341
MA0074.10.358953
MA0076.10.609177
MA0077.10.65962
MA0078.10.447828
MA0081.10.578007
MA0083.10.703169
MA0084.11.18798
MA0087.10.664629
MA0088.10.0514785
MA0089.10
MA0090.10.635809
MA0091.11.39427
MA0092.10.691297
MA0093.10.915249
MA0095.10
MA0098.10
MA0100.10.375452
MA0101.12.12227
MA0103.10.146091
MA0105.10.701161
MA0106.11.0329
MA0107.11.16768
MA0108.20.540797
MA0109.10
MA0111.10.660878
MA0113.10.414278
MA0114.10.104181
MA0115.10.929032
MA0116.10.10959
MA0117.10.732
MA0119.10.548507
MA0122.10.756889
MA0124.10.888592
MA0125.10.807083
MA0130.10
MA0131.10.464307
MA0132.10
MA0133.10
MA0135.10.725055
MA0136.10.369468
MA0139.10.0564547
MA0140.10.327488
MA0141.10.197753
MA0142.10.514195
MA0143.10.414436
MA0144.10.316332
MA0145.10.16253
MA0146.10.248894
MA0147.10.36013
MA0148.10.296708
MA0149.10.319221
MA0062.20.0599644
MA0035.20.326883
MA0039.20.00412151
MA0138.20.44894
MA0002.20.0708857
MA0137.20.168782
MA0104.20.561843
MA0047.21.00935
MA0112.21.10559
MA0065.20.16797
MA0150.11.17219
MA0151.10
MA0152.10.333125
MA0153.10.790794
MA0154.10.0872435
MA0155.10.0505475
MA0156.10.170442
MA0157.10.489002
MA0158.10
MA0159.10.361202
MA0160.10.30953
MA0161.10
MA0162.10.0826011
MA0163.10.0183776
MA0164.10.425415
MA0080.20.154815
MA0018.20.400879
MA0099.20.333432
MA0079.24.50435e-05
MA0102.21.22472
MA0258.11.04518
MA0259.10.117259
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
NFKB1#479072.744031712096920.006869951901034420.0290965126968707
POU2F2#545253.252187163479470.01362351556019460.0480733297831254



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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